Education Secretary Michael Gove is being urged to stop his officials using private emails for government business and to check the practice is curbed.
Information Commissioner Christopher Graham says the use of private emails and texts should be "actively discouraged".
His guidance follows reports private emails were used to conduct Department for Education(DfE) business.
The DfE denied the reports, insisting the emails were about Tory business.
The Information Commissioner has carried out his first ever probe of a government department under the Freedom of Information law following the reports.
He finds that while the FOI rules on the use of private emails are known within Mr Gove's department "it is not clear that this advice and guidance has been fully understood and followed by those covered by it."
The commissioner's decision to stage a "good practice visit" to the department stems from reports in the Financial Times in September about the use of private email by Michael Gove and his advisers.
The paper quotes an email from one of Education Secretary Mr Gove's special advisers, Dominic Cummings.
It says he will not answer emails to his official department account, but only those sent to a gmail account and urges the recipients to do likewise.
The DfE responded that the emails concerned the Conservative Party spring conference 2011 rather than government business.
"Mr Cummings was telling Conservative Party officials not to use his departmental account for political business. The FT story gives an entirely misleading impression of Mr Cummings' email," the statement said.
The commissioner is calling for Mr Gove's senior officials " to support the message that staff (in particular Special Advisers) may be asked to search their private email accounts when there is a reasonable possibility that information relating to government business may be held."
He adds: "Given the difficulty for civil servants and private offices to search private email accounts, and taking into account concerns regarding the security of these accounts and the need to ensure the completeness of the public record, the use of private email should continue to be actively discouraged."
The commissioner also calls for checks "across the department, including within private offices, to ensure policies, procedures and guidance in relation to information rights is being followed in practice."
Early in the New Year he will also rule on FoI requests to the department by the Financial Times.
In a separate move the commissioner has also reminded the whole public sector that private emails and texts are covered by FoI requests.
"It should not come as a surprise to public authorities to have the clarification that information held in private email accounts can be subject to Freedom of Information law if it relates to official business," he says.
"This has always been the case - the Act covers all recorded information in any form."
The BBC's Freedom of Information specialist Martin Rosenbaum says his comments may irritate those who find FOI requests a "source of aggravation".
He adds that doubtless all this will now result in numerous FOI requests for the texts and gmail messages of ministers and officials - but don't expect to be reading them soon.